The environmental ministers agreed to eight bans in five countries on genetically modified (GMO) maize and rapeseed types.
Between 1997 and 2000, Austria, France, Germany, Greece and Luxembourg banned specific GMOs - that had actually been cleared for entry into Europe- on their territory, in particular three maize and two rapeseed types.
But last week the Commission asked ministers to vote on endorsing an order to lift the bans within twenty days. Environmental ministers failed to tow the line, instead opting to back the national bans.
EU law provides for national GMO bans if the government can justify the prohibition.
"A very large majority, 22 member states, rejected proposals to lift these national bans," Luxembourg Environment minister Lucien Lux told a news conference.
Green groups, vociferous opponents to GM foodstuffs, rejoiced at the member's move.
"Today's vote results mark a historic turning point in the debate on genetically modified food and crops," says Eric Gall, Greenpeace policy adviser on GMOs.
The Commission must learn from today's lesson and stop hiding behind technocratic procedures and confidential expertise to force GMOs into our fields and supermarkets, he adds.
But the biotechnology industry was left deeply disappointed and despondent.
"Today's vote is another failure of member states to play by the rules that they themselves established.
The EU's approval process for safe GMOs is arguably the strictest in the world and these bans are not scientifically justifiable," argues Simon Barber, director of the plant biotechnology unit at EuropaBio, biotech's European industry association.
GM crops approved at a European level but banned in the five national states are Bayer CropScience T25 maize (28/04/2000), Syngenta Bt176 maize, Monsanto MON810 maize, Bayer CropScience oilseed rape and Topas 19/2 and MS1xRF1.
From 1998 to 2004 the EU imposed a ban on approving any new GM crops. Tough new rules on GM ingredient food labelling imposed last year have since cleared a way to end the ban, with a couple of new approvals already passed into the Official Journal.